Workshops buy inputs from the local market and sell their outputs back to the local market. If the inputs are available and cheap on the local market and the outputs are scarce and expensive on the local market, the workshop will make lots of money. If the inputs are not present or expensive, the shop will not run. If the outputs are present in too large a quantity and thus cheap on the local market, the shop will not make money.
As was said, exactly which types of shops are best in certain locations varies a bit based on what other shops are in the city and also in other cities nearby. This is because the other shops nearby will make more of the same output which will either be sold directly to the local market if the shop is in the same city or can be imported by caravan if nearby. However, the basic principles remain the same regardless of what type of shop you have.
As far as inputs, choosing a shop that uses inputs from the bound villages is a good starting point, but not strictly required. Caravans might import the inputs if they are made in nearby villages. Also, the total number of hearths that a village has affects the rate at which it creates goods. Theoretically, you can also import the inputs yourself and dump them on the local market. This is especially good if you manage to find them cheap somewhere else.
In regards to keeping the price of outputs high, there are at least 3 things to consider. First, caravans may buy the outputs and export them somewhere else. This will keep the local supply low and the price higher. However, you usually can't count on this because the caravans will generally only buy things when they start to get cheap in the first place.
Second, you can buy the outputs yourself. Just going to the town where your brewery is and buying all of the beer will have an immediate effect on the price of beer and should make your shop become more profitable relatively quickly. Now you have to go somewhere else and sell the beer, hopefully at a profit. (Also, your men will drink some of the beer along the way. That will help morale and potentially give your quartermaster extra steward skill). Keep in mind that the conditions that caused too much beer on the local market probably still exist so you will periodically have to return and buy up the beer again in order to keep your brewery profitable.
The final way for goods to be consumed is for the town itself to consume them. Basically, the local population does buy beer from the market. However, the rate at which the local population buys beer is related to the prosperity of the city. Prosperous cities drink more beer (and use more of pretty much everything in general). For this reason, it's generally better to have workshops in cities with high prosperity. The Sturgian cities all start with comparatively low prosperity. Thus, you should probably plan on returning regularly to Omor and Balgard to buy the beer and tools. If they (the cities) are kept safe for several years (don't get conquered), the prosperity in these cities will gradually rise and they may become more able to consume the outputs of your shops and keep the prices high enough to be profitable without intervention. There is a prosperity level where luxury consumption is triggered and shops become much more profitable because there is a step change in the local consumption (I believe this is at 5000 prosperity if I remember correctly).
The final thing to keep in mind is that shops have their own bank account (their capital). They try to keep the amount in their bank account to be around their "starting capital" which is usually 10,000. The amount in the account can be seen by going to the clan workshop screen and clicking on the workshop. If the amount is under the starting capital, the workshop will not pay you any of the profits even if the shop is profitable. Instead, the shop will keep the money in its own bank account in order to ride out future lulls in the local market. If the amount is above the starting capital it will pay you out some money each day. If the amount is significantly above the starting capital, it will pay you out more each day. Basically, you don't get the profit or loss from the shop every day. The profit or loss goes into the shops local capital account. Then, the shop pays you based on how much its local capital account is above the starting capital. This makes the profits from the shops a little more stable, but also means you need to pay closer attention to the shop since even after it starts having problems it might keep paying you some profits for some time (assuming it was profitable in the past).
